B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation

B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize1[W][OA]

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation

Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species

Transcript assemblies for representative transcripts generated in a joint assembly across 503 diverse maize inbred lines.

The assembly was generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file

Fragments per kilo base of exon model perl million fragments mapped (FPKM) values for 503 diverse maize inbred lines.

This file is a tab delimited file with a header line. The columns in the file are gene name, chromosome, gene start, and gene stop followed by the expression data for the 503 inbred lines

Genome wide association study (GWAS) results for growing degree days to pollen shed, growing degree days to silk, and last leaf with juvenile wax.

The file is a tab delimated file with a header that contains GWAS results presented as p-values for ~438K SNPs. The columns in the file are SNP, chromosome, position, growing degree days to pollen shed p- values, growing degree days to silk p-values, and last leaf with juvenile wax p-values

Imputed Genotype Scores 438K Single Nucleotide Polymorphisms across 503 diverse maize inbred lines

The file is a CSV file with a header that contains genotype scores imputed using GAPIT

Single Nucleotide Polymorphisms (SNPs) for 503 diverse maize inbred lines.

This is a tab delimited file with a header line that contains raw SNP data for 485,179 SNPs across 503 diverse maize inbred lines. The file contains a column for chromosome, position, the reference B73 v2 allele, number of missing data points, and observed alleles across the 503 inbred lines, followed by the data for the 503 inbred lines

Transcript assemblies for representative transcripts generated in individual assemblies for 366 diverse maize inbred lines.

The assemblies were generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file